Bacteriophage cell lysis of Shiga toxin-producing Escherichia coli for top-down proteomic identification of Shiga toxins 1 & 2 using matrix-assisted laser desorption/ionization tandem time-of-flight mass spectrometry

Colicin Immunity Proteins of Pathogenic Bacteria Detected by Antibiotic-Induced SOS Response, Plasmid Sequencing, MALDI-TOF-TOF Mass Spectrometry, and Top-Down Proteomic Analysis

RATIONALE

Plasmids can play a major role in the survival of pathogenic bacteria. Plasmids are acquired through horizontal gene transfer resulting in their spread across various strains, species and genera of bacteria. Colicins are bacterial protein toxins expressed by plasmid genes and released against co-located bacterial competitors.

METHODS

Three Shiga toxin-producing E. coli (STEC), whose genomes were sequenced previously, were analyzed using a combination of antibiotic induction, MALDI-TOF-TOF mass spectrometry, top-down proteomic analysis, and small plasmid sequencing. Protein biomarkers were identified using in-house software that matches protein mass and fragment ions of backbone cleavage by the aspartic acid effect. Predicted in silico protein structures assisted in the interpretation of protein ion fragmentation.

RESULTS

In addition to proteomic identification of phage-encoded Shiga toxin, we were able to identify plasmid-encoded immunity proteins for colicin D and E3. The genes for these plasmid-encoded proteins were not found in the previous genomic sequencing. However, resequencing of these strains for small plasmids revealed the genes to be present on 7-8 kb sized plasmids. Upstream of the colicin/immunity genes was an inverted repeat of the SOS/LexA box that represses gene expression until antibiotic challenge.

CONCLUSIONS

Our top-down proteomic method demonstrates that it is possible to screen putative pathogenic bacteria (whose genomes have been sequenced in full, in part or not at all) for the presence of phage- and plasmid-encoded toxin and colicin genes under SOS control. Small plasmid sequencing confirmed the presence of colicin/immunity genes (and their regulatory control) suggested from induction and top-down proteomic analysis.

Unusual modifications of protein biomarkers expressed by plasmid, prophage, and bacterial host of pathogenic Escherichia coli identified using top-down proteomic analysis

RATIONALE

Pathogenic bacteria often carry prophage (bacterial viruses) and plasmids (small circular pieces of DNA) that may harbor toxin, antibacterial, and antibiotic resistance genes. Proteomic characterization of pathogenic bacteria should include the identification of host proteins and proteins produced by prophage and plasmid genomes.

METHODS

Protein biomarkers of two strains of Shiga toxin-producing Escherichia coli (STEC) were identified using antibiotic induction, matrix-assisted laser desorption/ionization tandem time-of-flight (MALDI-TOF-TOF) tandem mass spectrometry (MS/MS) with post-source decay (PSD), top-down proteomic (TDP) analysis, and plasmid sequencing. Alphafold2 was also used to compare predicted in silico structures of the identified proteins to prominent fragment ions generated using MS/MS-PSD. Strain samples were also analyzed with and without chemical reduction treatment to detect the attachment of pendant groups bound by thioester or disulfide bonds.

RESULTS

Shiga toxin was detected and/or identified in both STEC strains. For the first time, we also identified the osmotically inducible protein (OsmY) whose sequence unexpectedly had two forms: a full and a truncated sequence. The truncated OsmY terminates in the middle of an α-helix as determined by Alphafold2. A plasmid-encoded colicin immunity protein was also identified with and without attachment of an unidentified cysteine-bound pendant group (~307 Da). Plasmid sequencing confirmed top-down analysis and the identification of a promoter upstream of the immunity gene that is activated by antibiotic induction, that is, SOS box.

CONCLUSIONS

TDP analysis, coupled with other techniques (e.g., antibiotic induction, chemical reduction, plasmid sequencing, and in silico protein modeling), is a powerful tool to identify proteins (and their modifications), including prophage- and plasmid-encoded proteins, produced by pathogenic microorganisms.

Isolation and pathogenicity evaluation of Escherichia coli O157:H7 from common carp, Cyprinus carpio

Escherichia coli O157:H7 is the primary serotype of enterohaemorrhagic E. coli (EHEC), which can cause diarrhea, hemorrhagic colitis, and hemolytic uremic syndrome. It is considered as a major health concern due to it being a zoonotic disease that is transmitted through food. In this study, a pathogenic bacterium was isolated from infected carp, which identified as E. coli O157:H7 named X21 through genetic sequencing, phylogenetic analysis, physiological and biochemical tests. In the experiment, crucian carp was used as a model to study the pathogenicity of the isolate, the pathological histological observations and cytokines expression of fish tissues were determined after bacterial challenge. The results showed that severe pathological damage observed in the liver, spleen, headkidney of fish infected with isolate X21. Besides, we found that accumulation of IgT+ B cells in the lamina propria of intestine, and up-regulation of SUCH-r, IL-1β, IL-10, IL-11, MyD88, and TNF-α gene in various tissues. After challenged, the survivability of crucian carp infected with isolate X21 stands at a mere 14.27%. To our knowledge, this is the first report that E. coli O157:H7 infected the freshwater fish C. carpio, which indicates that this bacterium is a potential threat to public health and freshwater fish aquaculture.

Toxin and phage production from pathogenic E. coli by antibiotic induction analyzed by chemical reduction, MALDI-TOF-TOF mass spectrometry and top-down proteomic analysis

RATIONALE

Shiga toxin-producing Escherichia coli (STEC) are an ongoing threat to public health and agriculture. Our laboratory has developed a rapid method for identification of Shiga toxin (Stx), bacteriophage, and host proteins produced from STEC. We demonstrate this technique on two genomically sequenced STEC O145:H28 strains linked to two major outbreaks of foodborne illness occurring in 2007 (Belgium) and 2010 (Arizona).

METHODS

Our approach was to induce expression of stx, prophage, and host genes by antibiotic exposure, chemically reduce samples, and identify protein biomarkers from unfractionated samples using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, tandem mass spectrometry (MS/MS), and post-source decay (PSD). The protein mass and prominent fragment ions were used to identify protein sequences using top-down proteomic software developed in-house. Prominent fragment ions are the result of polypeptide backbone cleavage resulting from the aspartic acid effect fragmentation mechanism.

RESULTS

The B-subunit of Stx and acid-stress proteins HdeA and HdeB were identified in both STEC strains in their intramolecular disulfide bond-intact and reduced states. In addition, two cysteine-containing phage tail proteins were detected and identified from the Arizona strain but only under reducing conditions, which suggests that bacteriophage complexes are bound by intermolecular disulfide bonds. An acyl carrier protein (ACP) and a phosphocarrier protein were also identified from the Belgium strain. ACP was post-translationally modified with attachment of a phosphopantetheine linker at residue S36. The abundance of ACP (plus linker) was significantly increased on chemical reduction, suggesting the release of fatty acids bound to the ACP + linker at a thioester bond. MS/MS-PSD revealed dissociative loss of the linker from the precursor ion as well as fragment ions with and without the attached linker consistent with its attachment at S36.

CONCLUSIONS

This study demonstrates the advantages of chemical reduction in facilitating the detection and top-down identification of protein biomarkers of pathogenic bacteria.

Top-down proteomic identification of plasmid and host proteins produced by pathogenic Escherichia coli using MALDI-TOF-TOF tandem mass spectrometry

Fourteen proteins produced by three pathogenic Escherichia coli strains were identified using antibiotic induction, MALDI-TOF-TOF tandem mass spectrometry (MS/MS) and top-down proteomic analysis using software developed in-house. Host proteins as well as plasmid proteins were identified. Mature, intact protein ions were fragmented by post-source decay (PSD), and prominent fragment ions resulted from the aspartic acid effect fragmentation mechanism wherein polypeptide backbone cleavage (PBC) occurs on the C-terminal side of aspartic acid (D), glutamic acid (E) and asparagine (N) residues. These highly specific MS/MS-PSD fragment ions were compared to b- and y-type fragment ions on the C-terminal side of D-, E- and N-residues of in silico protein sequences derived from whole genome sequencing. Nine proteins were found to be post-translationally modified with either removal of an N-terminal methionine or a signal peptide. The protein sequence truncation algorithm of our software correctly identified all full and truncated protein sequences. Truncated sequences were compared to those predicted by SignalP. Nearly complete concurrence was obtained except for one protein where SignalP mis-identified the cleavage site by one residue. Two proteins had intramolecular disulfide bonds that were inferred by the absence of PBC on the C-terminal side of a D-residue located within the disulfide loop. These results demonstrate the utility of MALDI-TOF-TOF for identification of full and truncated bacterial proteins.

Top-Down Proteomic Identification of Shiga Toxin 1 and 2 from Pathogenic Escherichia coli Using MALDI-TOF-TOF Tandem Mass Spectrometry

Shiga-toxin-producing Escherichia coli (STEC) are a burden on agriculture and a threat to public health. Rapid methods are needed to identify STEC strains and characterize the Shiga toxin (Stx) they produce. We analyzed three STEC strains for Stx expression, using antibiotic induction, matrix-assisted laser desorption/ionization time-of-flight-time-of-flight (MALDI-TOF-TOF) mass spectrometry, and top-down proteomic analysis. E. coli O157:H- strain 493/89 is a clinical isolate linked to an outbreak of hemolytic uremic syndrome (HUS) in Germany in the late 1980s. E. coli O145:H28 strains RM12367-C1 and RM14496-C1 were isolated from an agricultural region in California. The stx operon of the two environmental strains were determined by whole genome sequencing (WGS). STEC strain 493/89 expressed Shiga toxin 2a (Stx2a) as identified by tandem mass spectrometry (MS/MS) of its B-subunit that allowed identification of the type and subtype of the toxin. RM12367-C1 also expressed Stx2a as identified by its B-subunit. RM14496-C1 expressed Shiga toxin 1a (Stx1a) as identified from its B-subunit. The B-subunits of Stx1 and Stx2 both have an intramolecular disulfide bond. MS/MS was obtained on both the disulfide-bond-intact and disulfide-bond-reduced B-subunit, with the latter being used for top-down proteomic identification. Top-down proteomic analysis was consistent with WGS.

Top-down and middle-down proteomic analysis of Shiga toxin using MALDI-TOF-TOF mass spectrometry

The method describes a step-by-step process for analysis of putative Shiga toxin-producing Escherichia coli (STEC) for expression of Shiga toxin (Stx). The technique utilizes antibiotic induction, mass spectrometry and top-down/middle-down proteomic analysis. Stx expression is induced by overnight culturing of a STEC strain on Luria-Bertani agar (LBA) supplemented with DNA-damaging antibiotics. Culturing on agar media avoids sample contamination from salts, small molecules, peptides, etc. present in broth media that would interfere with protein ionization by matrix-assisted laser desorption/ionization (MALDI). No mechanical lysis of bacterial cells is required to release the toxin as the antibiotic triggers the lytic cycle of the bacteriophage resulting in toxin expression and bacterial cell lysis. Unfractionated samples are analyzed by MALDI-time-of-flight-time-of-flight (MALDI-TOF-TOF) mass spectrometry and tandem mass spectrometry (MS/MS) using post-source decay (PSD). New features of the method are the following. •Each putative STEC strain is systematically screened for toxin expression using two different antibiotics at two different concentrations: ciprofloxacin at 10 and 20 ng mL^-1 and mitomycin-C at 800 and 1200 ng mL^-1 to determine the optimal antibiotic and concentration for toxin expression for each strain.•The grid-to-source voltage of MALDI-TOF-TOF is optimized to maximize PSD efficiency.

Clinically-relevant Shiga toxin 2 subtypes from environmental Shiga toxin-producing Escherichia coli identified by top-down/middle-down proteomics and DNA sequencing

Thirty-five environmental isolates of Shiga toxin-producing Escherichia coli (STEC) were analyzed by MALDI-TOF-TOF mass spectrometry, top-down/middle-down proteomics and DNA sequencing. Clinically-relevant Shiga toxin 2 (Stx2) produced by these STEC strains were subtyped based on MS and MS/MS (tandem mass spectrometry) of the intact B-subunit (top-down) and A2 fragment (middle-down) of the A-subunit using antibiotic-induced protein expression. Antibiotic induction of Stx2 was found to be strain dependent. By proteomic analysis, seventeen strains were identified as Stx2a, six strains as Stx2c, four strains as either Stx2a or 2c and eight strains as either Stx2a, 2c or 2d. DNA sequencing indicated only stx _2a and stx _2c genes as being present in these strains. Weak induction of Stx2 for certain strains made it difficult to distinguish between clinical subtypes by proteomic analysis. Very weak toxin induction in eight strains was consistent with a ∼1300 bp transposon insertion in the stx _2c A-subunit gene identified by DNA sequencing. DNA sequencing also revealed the presence of two bacteriophage (BP) in three strains with a stx _2a gene in each BP genome. Middle-down proteomic analysis of the A2 fragment confirmed expression of two stx _2a genes present in one of these strains based on a slight difference in the amino acid sequence (D ↔ E substitution) in the two A2 fragments.